Friday Night Covid Plotting #40

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 wintertree 21 Aug 2021

Yet another week.  It's a bit like being stuck inside a time loop, except without the high capers.

England remains in much of the same holding pattern - cases stagnating at a reasonably high daily level, hospitalisations and deaths stagnating at their corresponding, much lower levels.  The latest ONS survey was out a few days ago and has 95% of people with antibodies [1].   The rate constant for cases continues to bob up and down slightly whilst hovering in very mild growth.

Interpreting the dashboard data I plot  is increasingly limited by it not being categorised according to vaccinated/unvaccinated.  From this data I have no idea what fraction of the cases are people getting breakthrough infections after vaccination and what fraction are the unvaccinated.  Anecdotal reports in the news and the data I’ve linked over the last couple of weeks from San Diego county all point towards unvaccinated people being the driver of cases, but it’s always dangerous to jump to the obvious conclusions based on anecdotes….  Please, please, please PHE categorise the data by vaccine status...

Scotland.  A couple of months ago I used “hold my beer…” as a title for one of the Scottish plots.  I should have saved if for this week.  Cases started rocketing a few days back in the data.  Across the whole dataset, cases are doubling every ~6 days all of a sudden.  I’ve done a new demographic plot from the NHS Scotland data [2].  The left hand side heat map is a bit deceptive because they’ve used some irregular sized ages bins (*).  There’s a spectacular rate of exponential growth in the 15 to 19 and 20 to 24 age bins, with cases in 20 to 24 doubling in less than 3 days.  Bonkers [3]. I don’t think this has ever been seen in the data anywhere in the UK at any point before.  It’s so exceptional that I’d want to see a full on panic stations from Scotland to understand it immediately, because poorly understood and rapid changes could signpost all sorts of bad things.  Hopefully it’s just what happens when nightclubs are re-opened in the middle of a pandemic with an estimated R0 of ~8 and when a reasonable fraction of their clientele haven’t been vaccinated.  The demographic data fits with this but in no way proves it.  It's such a disconnect from the other ages we might see some "forcing" of cases in older bands as a result of this - not normally visible in the demographic rate constant data.

Some discussion at the end of the last thread as to why there’s apparently such a crazy growth following the opening of Scottish nightclubs but not the English ones, especially given the similar antibody levels in the ONS survey.  As the survey points out clearly, immunity is a lot more complex than the question of “Got antibodies [yes/no]”.  Perhaps the infection granted immunity making the difference in England fell during the Euros, which stopped a lot sooner in Scotland.  Again, dangerous to jump to the obvious conclusions from insufficient data as it can lead to the real reasons being missed so I hope the public health bods north of the border are pouring through the contact tracing data and piecing this together.

Plot D1.c plot for Scotland has a much extended range on the colour bar vs the English plot as the maximum rate constant is more than that seen at any point in England at the national level.  Funny story - the growth was so large it broke my code measuring the rate constant (fitting an exponential to segments of the data; the initial estimate was too far from reality to get closure within the maximum number of evaluations set.  I keep meaning to move all these measurements to the 7-day method for something much more pure, simple and analytical...)

Link to previous thread: https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_39-...

[1] https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/con...

[2] https://www.opendata.nhs.scot/dataset/covid-19-in-scotland/resource/9393bd6...

[3]  youtube.com/watch?v=ISy0Hl0SBfg& [Dizzee Rascal - Bonkers]

(*) rant rant rant: why do PHE, the ONS, PHS  NHS England and NHS Scotland all use different age bins?  Maximum frustration and stands directly in the way of clear, insightful analysis.   It’s annoying for me but it’s worse hone it comes to limiting what can be prepared for people making actual decisions.  Would be great if data was all presented in a gridded format with axes for age (1 year bins, please), gender, vaccine status (where possible) etc.  There's some weird mentality with a lot of the data where it's partially analysed in the downloads - separate out the more "raw" data and the analysed data products.  

Post edited at 21:33

1
OP wintertree 21 Aug 2021
In reply to wintertree:

The English Plots

Cases continue their gradual rise, and hospitalisations follow.  With the recent ONS antibody survey it feels a bit incongruous that we’re not starting to see R forced to less than 1 by the level of adult immunity; perhaps R0 is way higher than the already high estimates, or perhaps there are network effects at play (whole transmissive chains with lower than the national average antibody level), or perhaps we’re starting to get a lot of breakthrough infections.  The later doesn’t feel likely with no clear change in the case:hospitalisation ratio.

  • Without data categorised by vaccination status, interpretation is severely limited.  
  • Still - rising infections and rising hospitalisations = not the best, hopefully rising immunity levels will start to reverse this within the next week or two…. If they don't then there's some serious questions that need addressing about our strategy (whatever that is)

Plot 9 shows that all the rate constants are in the doldrums, hovering around very small positive values.

  •  Even low rate exponential growth compounds however over enough time, and cases aren’t exactly starting from a low level…

1
OP wintertree 21 Aug 2021
In reply to wintertree:

The Scottish Plots

Referring back to D1.s in my first post, this bonkers growth in cases is mostly driven by the age ranges 15-24; I suspect but have no proof that it’s more 18-24 but the data is coarsely binned.

  • If it does extend down much below 18, that’s going to get another boost as the effect of schools returning feeds through
  • Once again, as with late June, eyes turn to the hospital admissions data over the next couple of weeks - with the big demographic shift this represents to cases, we would expect the hospitalisation rate to be lower than that from a couple of months ago…. 
  • Hopefully this growth is mostly related to nightclubs etc and is a self-limiting effect as immunity levels build…… ??  See the English D1.c demographic cases plot in a later post for some discussion about how there might have been an initial unsustained flurry of activity when clubs etc opened south of the border.
Post edited at 21:31

1
OP wintertree 21 Aug 2021
In reply to wintertree:

The Four Nations Plots

In addition to the stuff already covered, Northern Ireland looks to be making a break for growth in cases.  

Looking at plot 9x, the gradual dropping of restrictions is going worse - in terms of cases - everywhere except England. 

  • This seems to fit wit the idea that the big football associated wave of infections in England has put immunity where its needed to moderate case growth as restrictions are dropped, but that’s really just my hunch than in any way evidenced by this data.

1
OP wintertree 21 Aug 2021
In reply to wintertree:

The Demographic Plots (England)

As with the top level data, the demographic rate constants are in the doldrums hovering around mild growth/decay.  Still, at least one interesting feature.

  • I’ve put an annotated version of D1.c (England) in here; the growth in the young adult band was briefly strongest after nightclubs opened but it wasn’t sustained and was followed by a matching bit of decay; I do wonder if there was something of a mad rush when nightcblus opened and then it wound back a bit, perhaps the same might moderate the emerging case-pocalypse in Scotland.
  • P1.e and shows the demographics are still moving about a bit - shifting slightly younger now, but the shifting about is well below the age where it should impact hospitalisations or deaths.


1
OP wintertree 21 Aug 2021
In reply to wintertree:

English Regional Plots

Pretty much the same as last week, the early-to-rise regions in the UTLA plot still look to me like they want to have a similar total area to the other ones (these are cases/100k so normalised to population size).  They also look to be gradually decaying - excepting their perturbance coincident with the delta+football spike everywhere else.  So, in a very hunchy and proof free way, it feels to me like we're still teetering on the brink of immunity moderating growth; but without this data longitudinally by vaccine status it's hard to know which of the following we're expecting

  • Cases to go in to consistent decay as immunity limits R to be < 1
  • Cases to remain at this sort of level as we have breakthrough infection driving by slowly falling immunity, but hospitalisations to fall as breakthrough infections have better health outcomes than antibody-free infections
  • Something else entirely...

1
OP wintertree 21 Aug 2021
In reply to wintertree:

I was out for a long walk earlier.  Part of the walk crossed what must now be a 20 year old forest on an old industrial site.  The ash dieback was really visible with some fully dead trees and almost none unscathed.  Most were dead or had bushy foliage restricted to the central core of the trees.  So much for getting away from it all...  A graphic example of what unmitigated "let it rip" looks like, and there seem to be a lot of similar lessons over how this and how Covid came to be so much worse for the UK than they could have been.   

The planet is stressed, and it's not getting better out there.  It's never too late to start taking biosecurity seriously.   I did a lot of pondering on the subject of trees and the relative merits of re-wilding with regionally appropriate species vs a mix of trees drawn from internationally that hit the optimax between maintaining local ecosystems and being robust against the next century.   

Finally...  I'll re-post a message I put towards the end of #39:

An unusually clear and IMO accurate presentation of the questions around “normalising” this virus into circulation with all the others.

https://www.bbc.co.uk/news/health-58270098 

I thought the comments on “over vaccinating” whilst hypothetically sensible were in reality unjustified, pre-empting as they do the JCVI guidance.  My expectation there is that the criteria will be around a medical risk / benefit analysis rather than a blanket “boost everyone” approach. 

Post edited at 21:54

1
 Si dH 21 Aug 2021
In reply to wintertree:

Thanks again. Interesting that the vaccine plot seems to be showing gradually increasing first doses now. I noticed a few good days recently. (57000 today.) Can't imagine why... maybe we should have another bunfight over what is restricting vaccine take-up? It would make a change from masks or Scotland

I am struggling to see the yellow and blue lines in your utla plot, are you able to make them bold or something? (Edit - although, the most noticeable thing about locations in England over the last 2-3 weeks from the dashboard map has been just how similar case rates are around the country. We have never had things this uniform as far as I can remember, even when rates were mostly very low. It seems a first; I feel like that should be important.

Post edited at 22:06
 joem 21 Aug 2021
In reply to Si dH:

> Thanks again. Interesting that the vaccine plot seems to be showing gradually increasing first doses now. I noticed a few good days recently. (57000 today.) Can't imagine why... maybe we should have another bunfight over what is restricting vaccine take-up? It would make a change from masks or Scotland

Instinct says 16-18yr olds probably account for that.

 Si dH 21 Aug 2021
In reply to joem:

Of course, you will be right. It's late = slow of brain.

OP wintertree 21 Aug 2021
In reply to Si dH:

>  maybe we should have another bunfight over what is restricting vaccine take-up? It would make a change from masks or Scotland 

I rather linked your take which I termed an impedance mismatch, although the - important - question remains unanswered.  The demographic data might illuminate this but I've resisted analysing that; hopefully one of the Twitter covid data types will...

> I am struggling to see the yellow and blue lines in your utla plot, are you able to make them bold or something?

Ah, my bad.  There aren't any right now, but I haven't removed the generic legend entries.

> We have never had things this uniform as far as I can remember, even when rates were mostly very low. It seems a first; I feel like that should be important

One to cogitate on.

Post edited at 22:33
 joem 21 Aug 2021
In reply to Si dH:

Still think it’s weird that it was holding at a more or less fixed rate prior to this mind.

 Wicamoi 21 Aug 2021
In reply to wintertree:

Bravo again wintertree - and particularly the post to which I am replying. The ash dieback-Covid connection is compelling. I walked past some favourite old ash trees today, shrinking into themselves, dying.

OP wintertree 21 Aug 2021
In reply to Wicamoi:

Ive been trying for uplifting nature photos to combat the drudgery of these plots, but of a failure this week.  

It’s the ash dieback on my mind these last few months rather than covid - the trees defining the view from my windows, the trees along every road I drive and path I walk, the lay-by where my favourite burger wagon resides.  There’s a limestone gorge with mature ancient forest in our part of the world - Castle Eden Dene - that’s a fantastic visit in autumn, but I’m part dreading it this year.

The rowan trees are spectacular this year however, and the leading tree in my hazel orchard has its first crop - they’re on a four meter grid and I have a plan to shape them to make a vaulted undercroft beneath the canopies, and it’s starting to get to the point I can stake branches from two trees together.   I’ve also got a single gage - the first since I planted the tree - which I am looking forwards to eating immensely.  Having had a wild career pivot this last year, the idea of pivoting again in a few years to something involving trees doesn’t seem so impossible.


1
In reply to wintertree:

Schools went back in Scotland 16Aug / 17Aug depending on the area.  Your D1c plot with the blue bar coming back on younger ages after a gap over summer looks a lot like school holidays.  

I'm not sure what the policy is this term but it used to be 2 lateral flow tests a week.  If they handed out tests on the first day of term to all the kids and teachers it is going to cause a jump in the cases number because they'll be finding asymptomatic cases that would have been missed over summer.

2
 girlymonkey 22 Aug 2021
In reply to wintertree:

We know a family near to us (central Scotland) where mum and both teenagers have all just tested positive. Teenager 1 won't be vaccinated, and if teenager 2 has been, it will be too recent to take effect yet. Mum, however, has been. But she also came down with whooping cough a few years ago despite being vaccinated, which I find interesting. Makes me wonder if the break through infections might be in people who have previous history of break through infections to other vaccines? She has no underlying health conditions, as far as I am aware. 

Dad of the family seems fine, so far. 

Anyway, not that relevant really, but the link to other breakthrough infection piqued my interest.

 Si dH 22 Aug 2021
In reply to tom_in_edinburgh:

School testing raises case rates in the 0-14 age range substantially and the 15-19 range marginally (although, it's clearer when 0-4, 5-9 and 10-14 ranges are split.) The current increase in Scotland in 15-19 and 20-24 is much greater than in 0-14 so schools are not really a credible theory as the prime driver. I'm sure it contributes a bit though, and may do more over the next couple of weeks. Universities in Scotland haven't started to go back, right? I assume they start at a more similar time to those in England.

Post edited at 08:19
OP wintertree 22 Aug 2021
In reply to tom_in_edinburgh:

> Schools went back in Scotland 16Aug / 17Aug depending on the area.  Your D1c plot with the blue bar coming back on younger ages after a gap over summer looks a lot like school holidays.  

The change in rate constant is all ages, and concentrate in younger adults.  It corresponds to the football event as indicated by the gender signal.  I don’t think it’s connected to the school holidays much.

> I'm not sure what the policy is this term but it used to be 2 lateral flow tests a week.  If they handed out tests on the first day of term to all the kids and teachers it is going to cause a jump in the cases number because they'll be finding asymptomatic cases that would have been missed over summer.

This might show through over the next week; in the English data the “switch on” of PCR confirmed LFD data has been getting weaker each term - you can see it really clearly around late March 2021 in the English D1.c plot, then it weakens each subsequent term.  A corresponding effect is in the Scottish plot but is weaker.   I think the bigger issue with schools is going to be spread rather than asymptomatic “switch on”, but this term really is going to be very different to any other in the pandemic so we wait and see…

 neilh 22 Aug 2021
In reply to wintertree:

On the nightclub issue I have read that nightclubs are really struggling to attract punters and typically are only about 1/3 full. So it looks like people are voting with their feet so to speak. The other business issue is that they are not as popular now as they once were as people go for different forms of entertainment these days. My daughters for example never go , preferring late night night cafes/ bars. 
 

Festivals are far more popular. 
 

 Dr.S at work 22 Aug 2021
In reply to Si dH:

Re University’s - my course has a rolling final year so we have students almost all of the time, and it’s one of the courses that continued throughout the pandemic.  A five year course, so older students and very medically literate so I’d expect good vaccine uptake by now.

Anecdotally we have more students having infections now then at any point in the pandemic so far - so the change in restrictions plus delta will be ‘interesting’ once the new term starts for the majority.

OP wintertree 22 Aug 2021
In reply to Šljiva & neilh:

Re: the guardian article….Complaints from nightclub operators that mixed messaging from the government is confusing people and keeping them away - it’s not often that chaotic and mixed messaging works against the spread of the virus!

I have no idea how a vaccine passport scheme is going to come together in time for the deadline, one could be forgiven for thinking it’s all a marketing ploy and will be dropped.  I just can’t see something robust enough in terms of authenticity and operations on the door - then again I haven’t been in to an actual club for about 12 years so what do I know…

 elsewhere 22 Aug 2021
In reply to wintertree:

Authenticity - it doesn't have to be perfect but it does have to be workable and actually implemented at the door.

As long as it's easier to get the real certificate then the odd fake shouldn't matter. Like currencies or passports, if it's not worth faking it's not worth having!

Post edited at 13:48
 Si dH 22 Aug 2021
In reply to elsewhere:

I don't really understand the complaints from nightclub owners about operability or implementation. I don't remember ever going to a nightclub (I went to many) that didn't have bouncers on the door asking people for ID who they suspected of being underage. They don't really need anything new. If the vaccine certificate had DOB on it that would make their life easier because they could just demand that instead of having to decide the validity of various dodgy student ID cards like they always used to.

 minimike 22 Aug 2021
In reply to wintertree:

> The planet is stressed, and it's not getting better out there.  It's never too late to start taking biosecurity seriously.   I did a lot of pondering on the subject of trees and the relative merits of re-wilding with regionally appropriate species vs a mix of trees drawn from internationally that hit the optimax between maintaining local ecosystems and being robust against the next century.  

Monday night Armageddon plotting #01?

I feel Monday is most appropriate.. 

 elsewhere 22 Aug 2021

Today the news is reporting "first time cases", previously it was just "cases".

Is this significant?

 Si dH 22 Aug 2021
In reply to elsewhere:

> Today the news is reporting "first time cases", previously it was just "cases".

> Is this significant?

There is no change in the nature of the cases data reported on the dashboard today. So I suspect it's a case of misreporting. What was the news article you saw?

As it happens I was looking earlier at the latest variant technical briefing, which led me to an estimate of reinfections in the latest phe respiratory virus surveillance report. From a total of ~5.2 million pillar 1 and pillar 2 positive cases in England to their data date, there were approx 35000 possible reinfections, meaning people who have tested positive twice > 90 days apart.

There are one or two ongoing studies of NHS staff that get reported in these briefings looking for signs of increased infections in people who have had it before or/and been vaccinated. There are reinfections reported but the rate of them follows trends in national prevalence fairly clearly and isn't seemingly higher with Delta than it was with Alpha.

Post edited at 19:19
 Si dH 22 Aug 2021
In reply to wintertree:

You have said a few times that the dashboard data would be much more useful if it was split by vaccination status. What specifically would you be looking for?

I was thinking earlier that it would be possible with some manual data manipulation to estimate fractions of cases in vaccinated and unvaccinated people as a function of time at three-weekly intervals using the data in the variant technical briefings. They have the necessary data on them but it isn't presented straightforwardly. Although three-weekly is obviously far inferior to daily updates, it would be enough now to see any trends as they have been publishing the data for a few months.

 Šljiva 22 Aug 2021
In reply to wintertree: 

will shortly be heading off across several European countries with our masks and vaccine passports. I quite like the idea of the latter, will be interesting to see how it works in reality. 

Notable post-holiday Delta-getting-going pattern in parts of Europe … 

 elsewhere 22 Aug 2021
In reply to Si dH:

BBC 24 Hour news channel Freeview 231

OP wintertree 22 Aug 2021
In reply to Si dH:

> You have said a few times that the dashboard data would be much more useful if it was split by vaccination status. What specifically would you be looking for?

  1. To confirm the likely situation that the majority of the cases and almost all the hospitalisations are still amongst the unvaccinated
    • If this is true - and considering the studies on naturally acquired immunity and the re-infection data you've also mentioned today - then we expect the number of cases and more importantly hospitalisations to start falling very soon
    • If this is not true, and a lot of hospitalisations are of the vaccinated, we're looking at a major problem going forwards as schools turn on, then universities, then winter - all increasing spread and viral loads, and hospitalisation rates already being at an unsustainable level.  I think this is very unlikely based on the hodge-podge of data out there, but it would be nice to have a simple, hard plot to point at and say "this is just a phase we're going through...."
  2. Such data would provide an early warning sign for a more evasive variant as well as more of an understanding about what's potentially coming over winter in the absence of new variants.

> I was thinking earlier that it would be possible with some manual data manipulation to estimate fractions of cases in vaccinated and unvaccinated people as a function of time at three-weekly intervals using the data in the variant technical briefings. They have the necessary data on them but it isn't presented straightforwardly. Although three-weekly is obviously far inferior to daily updates, it would be enough now to see any trends as they have been publishing the data for a few months.

Interesting; if it's not a lot of work to tabulate the numbers in Excel and back out the numbers with some excel formula, that sounds like a rainy day project to me.  Some good weather ahead however!  This breakdown must surely be coming to the dashboard...  Ideally coded by each of the matrix of possibilities [vaccinated / not vaccinated] and [past PCR positive / first PCR positive.

In other news, was it you who posted a thread in The Pub in spring asking for an identity on two fruit tree blossoms?  If so, did it turn out to be an apple (probably red) and a plum?  Can't find the original thread...  My plums had their blossom trashed by a severe hail storm, I've got one gage and that's it.

Edit: You mentioned vaccinations rising in an early post; more of that today - eyeballing it it looks like the highest level of first doses in ~ 5 weeks.

In reply to elsewhere:

> Today the news is reporting "first time cases", previously it was just "cases".

Sounds like confusion to me, although without the news report to hand it's hard to say.  As Si dH said, there's no change to the dashboard and no "yellow banner" announcing changes to reporting.

In reply to kirsten:

> Notable post-holiday Delta-getting-going pattern in parts of Europe … 

There's quite a few places where things are taking a turn for the worse out there . Delta really is awful news coming before global vaccination is much more progressed.

In reply to bruxist (from plotting #39):

> I've just come to the end of two months based at local hospitals - am moonlighting away from academia in Public Health for the LA - and this week went back to the office. The morning I returned, my colleagues were participating in a 'well-being' event, meant to be some sort of post-pandemic spirit-builder, all indoors in one office room, mostly unmasked, with a buffet. I dodged the event.

Re: Working in a large organisation where people fail to "get it" en mass and are preparing to rush head long in to a lot of in-person teaching whilst still not getting it over ventilation....  What's you're secret to not having some sort of rage explosion amidst it all?  Asking for various colleagues...  

In reply to thread:

Another day of bonkers growth in the 7-day-change measure of the Scottish rate constant.  It is at least showing signs that the increase is coming to an end.   A doubling time of 5 days is still pretty drastic...  School data should start feeding through to this plot soon.  No sign of England joining the trend...

Post edited at 20:50

 bruxist 22 Aug 2021
In reply to wintertree:

> Re: Working in a large organisation where people fail to "get it" en mass and are preparing to rush head long in to a lot of in-person teaching whilst still not getting it over ventilation....  What's you're secret to not having some sort of rage explosion amidst it all?  Asking for various colleagues...  

Well, in a way I sympathize with them, despite keeping myself well out of what seems to me an obvious danger zone. It was much safer in the hospital! They've had a fantastically crap 18 months with no break, no furlough, being redeployed often into frontline service, having to learn new tricks that have often only been devised in haste the preceding evening - sorting out the vaccination booking procedures at the local hospitals in the months before there was a centralized NHS booking system was a real humdinger - and I can understand their sometimes desperate desire to feel that what they do for a living involves at least some joy rather than endless and unpredictable grind.

So I suppose I've concluded that tinkering around the unseen edges is a better use of my time, and keeps me from exploding at them. Getting the ventilation issues addressed with the building managers and Infection Control. Nudging staff towards KF94s/KN95s (mostly by giving them away or leaving boxes of them lying around). Making sure that the unions and H&S and HR are doing the things they need to do to mitigate the worst instincts of the staff. I doubt much of this would've been effective at uni, though, and think I'd have been having regular rage explosions and managed to paint a target on my back.

OP wintertree 22 Aug 2021
In reply to bruxist:

Ah, I was too opaque, I was wondering how you were surviving the university environment side.

It sounds like the LA and hospital staff are lucky to have you working on their behalf.  Best wishes for when you return to the other world.  After I left my office last March I realised there was no going back for me.

In reply to wintertree:

> The change in rate constant is all ages, and concentrate in younger adults.  It corresponds to the football event as indicated by the gender signal.  I don’t think it’s connected to the school holidays much.

OK.  But I am still saying the school holidays are the most likely cause for the very simple reason that not much else that could do it happened in the time period.   There wasn't a football championship.  Technically, there is an Edinburgh festival but I'd never have noticed except somebody mentioned it on here.  

This is only the second time we have seen back to school from summer holidays since the Corona epidemic started in the UK.   A lot of things were different last year so there's not much comparative data.

My guess is there's a fair number of things which are correlated with the end of school summer holidays e.g. timing of family holiday, kids who have moped about in their rooms over summer noticing they'll be back at school or uni soon and getting in some socialisation, back to school shopping, teachers getting tested before term, older siblings and parents getting tested after a school age kid gets a positive Linear Flow.

Post edited at 22:26
3
 bruxist 22 Aug 2021
In reply to wintertree:

>  After I left my office last March I realised there was no going back for me.

I haven't quite made my mind up, but I'm not sure I'm going to go back either. A lot of factors are in play: needing to be a carer for my elders, enjoying the immediate practical effects of what I do on the well-being of the local community, and discovering that being free of teaching, admin, and committee work means I'm doing more research than I ever did in post. The impending effects of climate change, too. I miss the teaching but have a nagging obscure feeling that there's more pressing work to be done.

 Si dH 22 Aug 2021
In reply to wintertree:

> Interesting; if it's not a lot of work to tabulate the numbers in Excel and back out the numbers with some excel formula, that sounds like a rainy day project to me.  Some good weather ahead however!  This breakdown must surely be coming to the dashboard...  Ideally coded by each of the matrix of possibilities [vaccinated / not vaccinated] and [past PCR positive / first PCR positive.

Here (see image) is my ham-fisted attempt. I hope/assume you can read the figures on a PC or tablet. I haven't graphed it because I'm useless at such things, and the trend at this level is obvious - the % of positive cases identified as the Delta variant in people who are fully vaccinated was just under 4% in late May, is increasing fairly continuously and now at just over 20%. The % figures for A&E visits are remarkably similar to those for cases, which I hadn't expected.

This data only includes cases that have been positively confirmed as Delta through sequencing or genotyping. I was going to read off the approx % of cases sequenced/genotyped in each period from the relevant report, but didn't get round to it. It dropped quite a lot in the recent wave.

Obviously the number of vaccinated people in the age groups who are more likely to get infected has increased a lot between May and August.

If this piques your interest, apart from presenting the data better I think the next logical step would be to somehow account for the changing % of the population that is vaccinated and see how this trend looked if one considered case rates per population instead of absolute case numbers.

The more recent reports also break the data down in to under and over 50 age bands, which I think changes the results a lot, but I have just lumped them together to keep it simple. The reports also provide separate data for A&E overnight stays and for deaths.

> In other news, was it you who posted a thread in The Pub in spring asking for an identity on two fruit tree blossoms?  If so, did it turn out to be an apple (probably red) and a plum?  Can't find the original thread...  My plums had their blossom trashed by a severe hail storm, I've got one gage and that's it.

Yes. The apple was right - that's doing well, although they are mixed red/green. The other one I thought we concluded was probably damson - but either way, not much is happening. I think it might have struggled in the heat but I'm a complete beginner in these things so I'm not sure if there is still any chance. I might have another closer look at it tomorrow.


OP wintertree 22 Aug 2021
In reply to Si dH:

Thanks for that table; interesting and at first glance a little concerning…

The next step for me would be to add a null hypothesis - “if the vaccine had no effect against this measure, what fraction of people would be fully vaccinated”.  This would just be the fraction of people with two doses three weeks (say) before the headline dates.  The other bounding hypothesis is that the vaccine has full effect, at which point the numbers are all 0%; where does reality fall between those two bounds?  

> Yes. The apple was right - that's doing well, although they are mixed red/green. The other one I thought we concluded was probably damson - but either way, not much is happening. I think it might have struggled in the heat but I'm a complete beginner in these things so I'm not sure if there is still any chance. I might have another closer look at it tomorrow.

If I did say damson and forgot it’s lost to the pub…. My experience of young damson trees is that if they know you want fruit, they’ll do bugger all.  Then I find some uncared for trees in a hedgerow, flailed yearly by the farmer and awash with them.  One harsh dry spell dried up the fruits on my damson and they all fell off at about 3 mm in size.  I’m going to have to extend the rainwater irrigation I think and get a bigger tank.

Post edited at 23:13
 Si dH 23 Aug 2021
In reply to wintertree:

> Thanks for that table; interesting and at first glance a little concerning…

> The next step for me would be to add a null hypothesis - “if the vaccine had no effect against this measure, what fraction of people would be fully vaccinated”.  This would just be the fraction of people with two doses three weeks (say) before the headline dates.  The other bounding hypothesis is that the vaccine has full effect, at which point the numbers are all 0%; where does reality fall between those two bounds?  

Agreed. The approximate range during the date range of interest is from 27.5% of England's total population double jabbed by 14 days before 25/05 (the first data point) to 57.1% 14 days before 15/08 (the last data point.)

So % of the total population who are fully jabbed has just more than doubled in the period. That wouldn't explain the magnitude of change in the data table above, but I think it's confounded by demographics. I.e. the increase in double vaxxed people is probably higher in the age groups who are more often infected.

It would probably be more useful to do the analysis with the two different age groupings (under and over 50) I think. The over 50 grouping will have much less change in vaccinated population during the period so it would help to verify any apparent trend.

Or you could produce a better null hypothesis by calculating population double vaxxed %s that are weighted by the cumulative infection rates in different age bands, if that makes sense.

Post edited at 08:17
 Offwidth 23 Aug 2021
In reply to Si dH:

Watched the Channel 4 documentary on the potential Wuhan lab leak last night. I found it very frustrating as it has very important and shocking information buried in a sea of one-sided views of the different expert opinions. Why 'sex something up' that is already a major scandal?

The big take-aways:

The Wuhan lab was working on gain of function research on bat virus (increasing transmitabillity and virulance) almost certainly using human adapted mice that could lead to a lab adapted virus with human to human transmission.

A significant amount of work was done in Biosafety level 2 facility (the rest in level 3 and apparently none in level 4).

The Wuhan researchers changed the name of a bat virus to try and hide a link to some fatalities in a Chinese mine.

Chinese officials denied any work was done with bats but the advertising of the Wuhan lab showed bats and the researchers had patented a new cage system for bats. Pure comedy totalitarian press handling.

Work was done with US collaboration and some US funding.  Fauci looks exceedingly economical with the truth when he said the US was not funding gain of function research in the Wuhan lab.

Not available on All 4 as yet but reported elsewhere:

https://inews.co.uk/news/politics/wuhan-lab-leak-explosive-channel-4-docume...

Post edited at 10:47
 Offwidth 23 Aug 2021
In reply to all

Latest Indie SAGE breifing with a simple look at herd immunity after the weekly data. They use R0 of 6 for delta.

youtube.com/watch?v=vgBF8ube3Ws&

The numbers for wintertree:

https://www.independentsage.org/wp-content/uploads/2021/08/LatestNumbers20A...

 Si dH 23 Aug 2021
In reply to Si dH:.

> Yes. The apple was right - that's doing well, although they are mixed red/green. The other one I thought we concluded was probably damson - but either way, not much is happening. I think it might have struggled in the heat but I'm a complete beginner in these things so I'm not sure if there is still any chance. I might have another closer look at it tomorrow.

One plum hiding under a bunch of leaves! Maybe 2cm across.


OP wintertree 23 Aug 2021
In reply to bruxist:

> I haven't quite made my mind up, but I'm not sure I'm going to go back either. A lot of factors are in play: needing to be a carer for my elders, enjoying the immediate practical effects of what I do on the well-being of the local community, and discovering that being free of teaching, admin, and committee work means I'm doing more research than I ever did in post. The impending effects of climate change, too. I miss the teaching but have a nagging obscure feeling that there's more pressing work to be done.

A lot of that sounds very familiar; loosing the teaching is a real shame although a wise person from this parish pointed out to me that going on to train recruits is not unlike 1:1 teaching of later years students.

In reply to Si dH:

> Agreed. The approximate range during the date range of interest is from 27.5% of England's total population double jabbed by 14 days before 25/05 (the first data point) to 57.1% 14 days before 15/08 (the last data point.)

Thanks - so the vaccine is making things a lot better, but not all the way better is my take from adding that to your table.

> [...] but I think it's confounded by demographics. I.e. the increase in double vaxxed people is probably higher in the age groups who are more often infected.

Yes, the demographic/time dependance makes much of this very tricky to gauge accurately.   

> Or you could produce a better null hypothesis by calculating population double vaxxed %s that are weighted by the cumulative infection rates in different age bands, if that makes sense.

I think it makes sense, and I think al the data is out there.  But my brain isn't thinking too well after a day on the road - furthest distance from the Wintertree bunker in 18 months, madness.

> One plum hiding under a bunch of leaves! Maybe 2cm across.

Excellent, I hope it doesn't split.  Plums fresh off a tree are hard to beat.  A couple of years ago I froze a Victoria plumb pulp after boiling and de-stoning them; trying to defrost it was maddening, it basically became Pykrete.  

In reply to Offwidth:

> Watched the Channel 4 documentary on the potential Wuhan lab leak last night. 

Thanks for the summary; watching these things for me is like having teeth pulled.  I miss the heydays of Tomorrow's World and Horizon before they went downhill.  I still think the mushroom principle is firmly in play here, it'll be interesting to see what eventually comes out.  Seems like sending NIH funding abroad became much more difficult around the time Trump would have been exposed to any classified information on all this; at the time a lot of it was put down to jingoism but I do wonder.

Thanks for the link to the Indie SAGE presentation source; I saw you posted their latest herd immunity estimates to the other thread in the pub.  Those estimates to me are the beginning of the next steps, not the end,  as a mild infection with Delta following vaccination is going to change a person's efficacy number, which will change things hopefully for the better, but with a bit more cat-and-mouse variation going on it does seem like elimination is fully off the cards.    Then again we live with dozens of other circulating viruses for which elimination is also off the cards.  They don't tend to hospitalise people at anything like the current Covid rate...  

In reply to thread:

Some updated plots.  

The rise in rate constants for Scotland continues to stagnate; I wonder if we're going to see it drop back down now towards 0- that would fit with the idea of a one-off rush to the nightclubs when they opened (backed by the largest rise being in ages 20-24.)  There was a lot of coverage of mad busy opening nights in England, and it sounds like now the clubs are struggling.  It had been bothering me that there was no corresponding spike in our data, but kirsten pointed out on #39 that it would have fallen as we had the separate, seismic level drop in rate constants going on from the end of the Euros, so there could have been some masking effect in England.  It's been suggested that the recent rise in Scotland is a "switch on" of asymptomatic LFD testing associated with schools but I'm far from convinced that sits well with the demographic data or with comparison to past switch ons in the English demographic data; if something similar starts to happen with next week's English data that would fit with the LFD theory, but I'll be eating my hat if that happens.

Interestingly there's a rise emerging in the ages 15-20 band for England.  Might be real, might be noise - we'll see when we get to the next thread.  I don't know if the LFDs have fired up already for schools; seems a bit early...?  Other respiratory viruses are starting to rise in this age band (going off DataMart stuff in recent PHE Surveillance Reports).

Post edited at 21:45

 Bottom Clinger 23 Aug 2021
In reply to Si dH:

I’ve foraged 18 pounds of lovely juicy tasty plums. I have a litter picker which I botched up a two foot extension to reach those normally out of reach. It’s an odd tree: two thirds have green leaves and no fruit, one third has almost purple leaves with crimson fruits. It will be wine in two years time - might try a sparkly. 

OP wintertree 23 Aug 2021
In reply to Bottom Clinger:

> I’ve foraged 18 pounds of lovely juicy tasty plums. I have a litter picker which I botched up a two foot extension to reach those normally out of reach. It’s an odd tree: two thirds have green leaves and no fruit, one third has almost purple leaves with crimson fruits. It will be wine in two years time - might try a sparkly. 

I don't have much to say other than that I'm immensely jealous, but replying will give the person who is systematically disliking all my posts a chance to mash their mouse button one more time...  I've been wondering about a plum picking invention; we have an apple picker which is an open metal lattice on a pole with some foam in it, the metal pieces bend over, you snuggle an apple between them and yank down.  Works a treat.

1
 Wingnut 23 Aug 2021
In reply to wintertree:

>>plum picking invention

My dad always did it with a ladder, a long-handled rake and us kids stood underneath to catch the results. The plums didn't end up in perfect condition, but were still fine for crumble, jam, or being immediately scoffed by kids who hadn't been fed for at least half an hour and hence were starving to death, honest, Dad!

 Šljiva 24 Aug 2021
In reply to wintertree:

Morning reading (time to remind us the virus is still around?) : 

https://www.theguardian.com/uk-news/2021/aug/23/uk-covid-deaths-hit-100-a-d...

https://www.theguardian.com/uk-news/2021/aug/23/almost-5000-covid-cases-lin...

https://www.theguardian.com/news/2021/aug/24/covid-19-seasonal-pattern-flu-...

on the other matter, we'll be cooking up the plums (and apples) from the in-laws' garden into plum (and apple) brandy, but that's sadly not legal here.

Post edited at 07:26
1
 Si dH 24 Aug 2021
In reply to Šljiva:

> Morning reading (time to remind us the virus is still around?) : 

Interesting, I noticed cases were rising a lot in the south west a couple of days ago (a few hours after suggesting on here that everything looked a bit uniform...) Perhaps this also explains some of the rise WT sees in the 15-20 age band.

 Šljiva 24 Aug 2021
In reply to Si dH:

I was idly wondering how many people would travel from Scotland to Cornwall. But either way seems a lot of cases for what I presume was mostly an outdoors event, no?  

Posting this one up again as well: https://graphics.reuters.com/world-coronavirus-tracker-and-maps/   

OP wintertree 24 Aug 2021
In reply to Šljiva:

> [...]

> But either way seems a lot of cases for what I presume was mostly an outdoors event, no?  

Looking at that photo of everyone crowded in by the stage, it's not hard to imaging "nearest neighbour" transmission as over those lengths scales it's almost indoors...  Especially if people are shouting/singing (exhalate) and dancing (higher respiration, more goes in and out).

The article raised a more important question for me though - how to the Gorillaz appear live on stage?

In reply to Wingnut:

Interesting, I hadn't considered the use of child fruit catchers; I could do with a larger family... Some some friends in plums for use of theirs, if my trees ever come in to their own...

 In reply to Si dH:

> Interesting, I noticed cases were rising a lot in the south west a couple of days ago

I should dust off the UTLA mapping code and see what it looks like...

 Šljiva 24 Aug 2021
In reply to wintertree:

Looking at that photo of everyone crowded in by the stage, it's not hard to imaging "nearest neighbour" transmission as over those lengths scales it's almost indoors...  Especially if people are shouting/singing (exhalate) and dancing (higher respiration, more goes in and out).

But ie Download only generated c 80 cases /10k attendees...

OP wintertree 24 Aug 2021
In reply to Šljiva:

> But ie Download only generated c 80 cases /10k attendees...

Cases were much lower then and from the behaviour of the cases plot I'm presuming (haven't looked for data) that Delta hadn't really hit Ireland then?  Delta has a much higher R0, probably not good for the most crowded sorts of outdoors interaction.

Post edited at 09:51
 MG 24 Aug 2021
In reply to wintertree:

> Interesting, I hadn't considered the use of child fruit catchers; I could do with a larger family... Some some friends in plums for use of theirs, if my trees ever come in to their own...

I think the traditional approach was to have "laddermen" who put a ladder up a tree.  Several pickers went up and stayed in the tree picking while the ladder was moved to another tree.  When the first tree was finished the laddermen went back and collected for pickers.  Etc over an entire orchard.

 Bottom Clinger 24 Aug 2021
In reply to wintertree:

Did you see my photo last year of my Apple picker?  Hilariously huge. Combined with my extended litter picker and beach combed boat hook, no fruit is safe. 
 

In reply to wintertree:

> I've been wondering about a plum picking invention;

Hard to believe you won't have been here already, but: https://www.thingiverse.com/tag:fruit_picker

 Toerag 24 Aug 2021
In reply to wintertree:

>  There was a lot of coverage of mad busy opening nights in England, and it sounds like now the clubs are struggling.

If it's anything like here then this is to be expected (we've had nightclubs open since we eliminated our first wave last summer).  The cost of drinks in pubs & clubs has increased significantly here since the start of the pandemic to the point that a LOT of young people simply cannot afford to go out as often as they used to.  Add to that the disproportionate employment hit on the young workforce (in employment terms) reducing their disposable income. There are generally two sorts of clubbers - those that are into the music and go to specific clubs to see specific DJs, and those that go at the end of a night's drinking because their mates decide to go.  That second group of 'casual clubbers' seem to be well down in numbers.  There's also potential clubbers avoiding going out because they don't want to jeopardise other activities like holidays.

 Toerag 24 Aug 2021
In reply to wintertree:

>   Please, please, please PHE categorise the data by vaccine status...

This is kind-of done here. All cases are listed out by vax status as follows:-

"Since the end of the second wave there have been 358 cases. Of these cases, 135 were unvaccinated, 40 were partially vaccinated, 183 were fully vaccinated (2 doses + 2 weeks soak time)."

What we don't know is the demographics or if they're incoming travellers or not. What we do know is that 88% of over 18s are fully vaxxed, 5% partially vaxxed and 7% are un-vaxxed. 35% of 16/17yr olds have had a single dose (the current JVCI recommendation - the heart muscle side effect seems to come after 2 doses).

We are still completely unrestricted on-island (I've been clubbing twice last weekend, and on the biggest Scout camp in Europe this summer at the weekend). Case numbers are rising, but very slowly. No doubt some are being hidden by people not wanting to be tested, but there's little cause for concern at present.

 Wicamoi 24 Aug 2021
In reply to wintertree:

Another grim data release from Scotland today. Cases almost back to the recent July peak (and thus much higher than the Jan peak, and the number reported today is actually the highest of the whole pandemic. Test positivity rate is just about the highest ever reported (narrowly beaten by three or four days in Jan 21). Cases rising in all age groups, but still led by 15-19 and 20-24.

In reply to Wicamoi:

Looking warm this week. I'm going to predict {gasp} a drop in rates coming soon.

 Wicamoi 24 Aug 2021
In reply to Longsufferingropeholder:

How soon?

In reply to Wicamoi:

Steady on. I'm not Nostradamus.
Let's just keep an eye on things next week, eh?

 Mark Edwards 24 Aug 2021
In reply to wintertree:

I just had an email from the Covid Survey. Now I can get my results by email instead of letters (one for swab and one for antibodies). On my next visit “your study worker will check and confirm your email address”. I’m reading this on my email account which is also where they send the vouchers! OK, maybe that’s just me, but this is what I found interesting:

“We hope this helps make your experience on the survey better. Together with around 400,000 other people ...”

So that’s the sample size for the ONS data (I was wondering).

OP wintertree 24 Aug 2021
In reply to Mark Edwards:

> “We hope this helps make your experience on the survey better. Together with around 400,000 other people ...”  So that’s the sample size for the ONS data (I was wondering).

Interesting; thanks for sharing.  That's a monumental undertaking and an incredibly useful dataset.

In reply to Wicamoi:

> Another grim data release from Scotland today. Cases almost back to the recent July peak (and thus much higher than the Jan peak, and the number reported today is actually the highest of the whole pandemic. Test positivity rate is just about the highest ever reported (narrowly beaten by three or four days in Jan 21). Cases rising in all age groups, but still led by 15-19 and 20-24.

The less bad news is that the rate constant measurements are still doing a good impression of turning a corner towards more moderate growth or at least decay - still a long way for them to fall, and a much higher baseline of cases locked in for the continued growth in the mean time. Speculating rampantly that an initial rush to nightclubs was a core issue here, hopefully the rate constant will be heading back towards 0....  Schools should be feeding through over the coming days, as well as hospitalisations - hopefully a small change for the later given the demographics.  If that's the case this is more of a "rapid antibody delivery event"  than a major problem....  If.

> Looking warm this week. I'm going to predict {gasp} a drop in rates coming soon.

Really nice few days just passed as well.

In reply to Toerag:

>   That second group of 'casual clubbers' seem to be well down in numbers.  There's also potential clubbers avoiding going out because they don't want to jeopardise other activities like holidays.

Changing times...  

> This is kind-of done here. All cases are listed out by vax status as follows:-  "Since the end of the second wave there have been 358 cases. Of these cases, 135 were unvaccinated, 40 were partially vaccinated, 183 were fully vaccinated (2 doses + 2 weeks soak time)."

I missed the part where the bailiwick opened up and let it in - was it a difficult choice or just a case of "let's do this then?".  Or was it forced by Delta?  Any breakdown on the hospitalisations by vaccine status?

In reply to MG:

> I think the traditional approach was to have "laddermen" who put a ladder up a tree.  Several pickers went up and stayed in the tree picking while the ladder was moved to another tree.  When the first tree was finished the laddermen went back and collected for pickers.  Etc over an entire orchard.

Excellent, those were the days.  I should spend more time studying orchard techniques I think.  I'm currently wondering if I should dig out and mulch circles around the trees, and also thinking about bunny control...

In reply to kirsten:

I can't immediately find the post but you suggested a few days ago that articles were coming out to soften people up for more restrictions.  If that's a spider sense, it's probably gone up a notch today...?


 Šljiva 24 Aug 2021
In reply to wintertree:

I wouldn’t expect more restrictions….yet, but maybe just a friendly nudge that all is not back to normal? After all, the government seemed quite relaxed about getting to 100k  cases a day not that long ago… 

 MG 24 Aug 2021

.

> Excellent, those were the days.  I should spend more time studying orchard techniques I think.  I'm currently wondering if I should dig out and mulch circles around the trees, and also thinking about bunny control...

I have mulch around all ours and manure/ compost underneath. Most are now 2-3 years old I wish they would hurry up and grow more! Just had 10 plums, James Grieve are edible now and Laxton Superb  are coming along. I'll need a dish that requires three damsons.in a month!

 Misha 24 Aug 2021
In reply to Toerag:

I wonder if there’s also an element of more younger people heading outdoors to get pissed in a tent or a van etc - something people did while night clubs etc were closed and some of those habits have stuck perhaps. Probably only a small effect from this though. 

 Wicamoi 24 Aug 2021
In reply to wintertree:

Thanks for the rate constants plot - it is a comfort. My gut feeling also aligns with LSRH's. Today was the best day of weather here for what's feels like weeks, and more of it forecast. Climbing tomorrow.

 KeyserSoze 25 Aug 2021
In reply to Misha:

> I wonder if there’s also an element of more younger people heading outdoors to get pissed in a tent or a van etc - something people did while night clubs etc were closed and some of those habits have stuck perhaps. Probably only a small effect from this though. 

Seems to me there is a lot of narrative fallacy going on.

We’re psychologically biased in seeking clear cause and effect, and it’s always reassuring to stick a story to a few data points in times of uncertainty.

However a lot of the variation outside of the longer trends might just as well be the result of a chaotic mishmash of thousands of variables, and quite a random process.

Post edited at 01:26
6
OP wintertree 25 Aug 2021
In reply to thread:

A Twitter post from Jeff Foust gives some insight in to how things are going  in the US:.  LOX demand from Covid is perhaps limiting space flight activities.   

Shotwell says one supply chain issue for SpaceX is a lack of liquid oxygen because of demands to treat COVID-19 patients. Will impact launch plans, she says.

https://mobile.twitter.com/jeff_foust?ref_src=twsrc%5Egoogle%7Ctwcamp%5Eser...

LOX shortage also putting municipal water treatment at risk

https://thehill.com/homenews/state-watch/568858-orlando-mayor-says-covid-19...

Looking at the daily cases, I’d expect hospital occupancy to keep rising in Florida for at least another two weeks.  

“Treat the unvaccinated” vs “have safe, clean drinking water for everyone” isn’t something I had expected, and doesn’t seem like it belongs on the “problems” list for a highly developed nation.

OP wintertree 25 Aug 2021
In reply to MG:

> I have mulch around all ours and manure/ compost underneath. Most are now 2-3 years old I wish they would hurry up and grow more!

I think I’m going to do that this year.  Maybe on half of them.

Ours range 3-5 years and likewise need to hurry up.  I’ve been doing a lot of pruning on the plums to get them in to “inverted hollow bell” shapes, I’m going to lay of for a couple of years and see if more fruit comes through.

>  I'll need a dish that requires three damsons.in a month!

I can suggest one for a salad involving two damsons and a carrot?   If I had but 3 I’d be tempted to do a starter with some cheese cubes of my preference, some mellon balls and quartered damsons, each to be wrapped in decent cured meat immediately prior to eating.

Touring a local orchard last week I saw a medlar tree, really interesting fruit - half way between one of those giant rosehips and an apple, helps to see how the species all relate.

 bridgstarr 25 Aug 2021
In reply to wintertree:

I am the most spectacularly poor gardener, except it seems when it comes to plums. I have one plum tree and its collapsing under the weight of its fruit

There's going to be a winter's worth of jam this year

 Bottom Clinger 25 Aug 2021
In reply to Toerag:

Do they produce data on “percentage of people in hospital with Covid who have been vaccinated” and “percentage of people who have died who have been vaccinated” ?

 Bottom Clinger 25 Aug 2021
In reply to KeyserSoze:

The England Italy footie final has been linked with 3,500 infections. 60,000 fans were present. Man Utd vs Leeds had 72,000 fans present. Mate is season ticket holder at Stretford end and said the concourse was rammed, zero mask wearing. I reckon in a few weeks PHE will release some info on football attendance and Covid spread. 

Loads of folk catching it now might not be a bad thing (building up immunity before winter). 

 Si dH 25 Aug 2021
In reply to Bottom Clinger:

> Do they produce data on “percentage of people in hospital with Covid who have been vaccinated” and “percentage of people who have died who have been vaccinated” ?

I provided this data for England hospitalisations higher up the thread (22:51 on Sunday.) The same source provides deaths data. The only shortfall is that it only covers cases that have been positively identified as Delta through sequencing, but that's still a large number and should extrapolate to the wider population fairly straightforwardly (I don't think there is anything about the selection of cases for sequencing that would bias the results significantly.)

(Edit, The answer is that the proportion of hospitalised patients who are fully vaccinated is increasing with time, which is my obviously either partly or wholly because of the increase in proportion of the population who are fully vaccinated. As of 15/08, it stood at a cumulative 21%. So, higher than that for a 'live' % now.)

Post edited at 10:24
 Bottom Clinger 25 Aug 2021
In reply to bridgstarr:

Plum wine is the way to go and is one of my favourite light coloured wines. Use more fruit than recipes say, and make spritzers with it.
 

I need to offload demijohns if anyone needs any (60 is too many!). 

 bridgstarr 25 Aug 2021
In reply to Bottom Clinger:

I've been making alcohol till it comes out of my ears, which is not great for my health. So I'm off the grog for the meantime. Although I might give it a bit of a whirl, just in case I get back on it. If you were round the corner I'd happily lighten your demijohn load but I think you're NW aren't you?

 Bottom Clinger 25 Aug 2021
In reply to bridgstarr:

Wigan, one mile from M6 Standish junction if you’re ever passing.
 

I could hide them in the undergrowth on the hard shoulder - you’d only have to slow down a bit - “hook a duck” style. 

 Bottom Clinger 25 Aug 2021
In reply to Si dH:

Thanks for this. Been busier than normal * so paying less attention to this stuff. 

Was on the radio yesterday talking about the Afghanistan crisis. 

OP wintertree 25 Aug 2021
In reply to Šljiva:

> I wouldn’t expect more restrictions….yet, but maybe just a friendly nudge that all is not back to normal? After all, the government seemed quite relaxed about getting to 100k  cases a day not that long ago… 

Sorry I got your take wrong!

I think how relaxed they are is going to depend a lot on what happens with the Scottish hospital data over the next week; to my eye it looks like the up-tick has just started, will take a while yet for them to get a good understanding of the case hospitalisation ratio of this new youthful phase.  Harder for us to get that rate without the longitudinal data.

On a tangent...

Some insightful comments from a JCVI member today - https://www.bbc.co.uk/news/live/uk-58326657

One quote:

Prof Finn says the myocarditis risk after second jabs in males is "indeed a concern" and is influencing the Joint Committee on Vaccination and Immunisation's decision making, particularly in the very young, where the risk of serious disease is much lower. 

There were several people on here and plenty elsewhere making a lot of noise about very low probability side effects from the AZ vaccine, that were orders of magnitude lower than the risk posed by the virus at its then levels, let alone what's happened since.

All those voices have been and remain silent over the parallel circumstance with Pfizer.  Whilst it appears to be a lower risk side effect, the benefit of the vaccine in the young is orders of magnitude lower, so the same questions arise.  

A few posters of quite varied stances have suggested some of the noise could be mistaken for a PR job against AZ, with them being the only major supplier to be undertaking the vaccine production on a non-profit basis.  A decision that senior management must be questioning very carefully, given the opportunity costs of taking this work.  Since the paper came out on the splicing codons and the DNA vaccines, it's not a stretch to imagine that AZ will soon have a version with the cause of their very low probability side effect removed.  That would put another option on the table should a variant emerge that's more lethal in younger adults.

 Bottom Clinger 25 Aug 2021
In reply to Si dH and anyone

I good few weeks back I posted a chart with Greater Manc Covid rates and England’s, and questioned would England move up the league and could this be a sign of infection acquired immunity.  This is the most recent chart, England is creeping up.


 Si dH 25 Aug 2021
In reply to Bottom Clinger:

I noticed in the phe flu and covid surveillance report this week (which I think WT also looks at sometimes) that they reported antibody survey results from blood tests done on blood donors (these are separate tests from the ONS surveys) for both spike proteins and other proteins separately; the point being that the vaccine only targets the spike, so people with other antibodies (N type I think) must have been infected.

They caveated the absolute numbers heavily because they think blood donors are more likely to be vaccinated and probably less likely to be infected than the population average. But regional differences should extrapolate. Pages 66-70:

https://www.gov.uk/government/statistics/national-flu-and-covid-19-surveill...

Using a rolling 12-week average of antibody measurements, London has the highest measured proportion of blood donors with antibodies that can only be due to natural covid infection (~23%), then North West (~19%), then midlands/NE& Yorkshire/East of England all fairly similar (~15%), South East a bit lower (~11%) and the South West a bit lower again (~9%).

Those are averaged over all ages.

At the moment, very broadly from dashboard data, case rates seem to be falling in London, steady in most of the north, rising in the midlands and the south (outside London.) All the changes are gradual except in the south west. It's probably a bit speculative to draw a hard link to the data above...

Post edited at 13:06
 Bottom Clinger 25 Aug 2021
In reply to Si dH:

Interesting stuff.  As someone who used to like a wee flutter, I do like to speculate, and noticed recently  how SW England now has higher Covid rates than Usual Suspect areas (no doubt partly due to it being a holiday area), but interesting nonetheless. 

 mondite 25 Aug 2021
In reply to Bottom Clinger:

> The England Italy footie final has been linked with 3,500 infections. 60,000 fans were present. Man Utd vs Leeds had 72,000 fans present. Mate is season ticket holder at Stretford end and said the concourse was rammed, zero mask wearing.

Was on train stopping at Finsbury Park after the Arsenal game on Sunday. Was rammed with minimal mask wearing.

OP wintertree 25 Aug 2021
In reply to Si dH:

> I noticed in the phe flu and covid surveillance report this week (which I think WT also looks at sometimes)

I've mostly been skimming the section on other respiratory viruses and wondering what the rise in those is doing to PCR testing rates given the overlap in symptoms.  Looks like I've missed out.... !

> that they reported antibody survey results from blood tests done on blood donors (these are separate tests from the ONS surveys) for both spike proteins and other proteins separately; the point being that the vaccine only targets the spike, so people with other antibodies (N type I think) must have been infected.

Fantastic!  I've been quietly hoping the ONS will upgrade to either this or a spike version detector.  

>  It's probably a bit speculative to draw a hard link to the data above...

Well, the data doesn't go against the more optimistic interpretations of where we are, so I'll take what I can get...

It would be very interesting to see corresponding data for Scotland...

In reply to any other of Rom's accounts still reading:

> Seems to me there is a lot of narrative fallacy going on.

I credit those on here with the nous to understand the way in which speculative ideas are being discussed; sometimes they can be tested against the data, sometimes they can't.  I think your pop psychology is as wide of the mark.  You seem a bit unaware of how much has been put together on some of the mechanisms at work by the posters to these threads.   

In reply to thread:

Updated plots.

  • English rate constant continues to hover around 0.  
  • Scottish rate constant has stagnated at a very high level, but it often does that on the timescale of days, not the drop I'd hoped to see.  
  • Looks to my eye like the corresponding rise in hospital admissions is starting to poke out of the noise.  Another week of data and the correspond Lissajous plot might be informative.  
  • Squint at the vaccine plot and last week was a standout level for at least 5 weeks, hopefully more of that this week. 

 bruxist 25 Aug 2021
In reply to wintertree:

> > Seems to me there is a lot of narrative fallacy going on.

> I credit those on here with the nous to understand the way in which speculative ideas are being discussed; sometimes they can be tested against the data, sometimes they can't.  I think your pop psychology is as wide of the mark.  You seem a bit unaware of how much has been put together on some of the mechanisms at work by the posters to these threads.   

Glad you spotted this. I was about to point out that the 'narrative fallacy' is a profoundly silly, made-up fallacy, being self-invalidating because it is, er, an example of the thing it purports to describe.

Narratologists naturally don't hold much brief for such tautologies, as they're the least systematic and least referential way of expressing meaning possible: though they're usually deliberately contrived to deny the possibility of meaning, their entire point is that they can tell us nothing about the world in which we live or the means, linguistic or otherwise, we use to understand that world.

1
OP wintertree 25 Aug 2021
In reply to bruxist:

> Glad you spotted this. I was about to point out that the 'narrative fallacy' is a profoundly silly, made-up fallacy, being self-invalidating because it is, er, an example of the thing it purports to describe.

I'd not heard of it before.  A quick bit of googling later and it seems that it's tied up in a pop science interpretation of chaos theory, in particular as applied to financial markets.  Here, we have Rom alluding that these random and (mathematically) chaotic effects dominate the medium and higher frequency bands of the data ("However a lot of the variation outside of the longer trends might just as well be the result of a chaotic mishmash of thousands of variables, and quite a random process."

What's notable about this is that a totally unrelated poster was insisting on much the same take during plotting #39 by drawing an analogy to financial markets (e.g. "Covid looks to me to have similar properties to turbulent markets") and arguing that this would likely dominate the data, particularly away from long term trends going forwards.

I've often thought it's funny how ideas suddenly come in to fashion across totally unrelated people, a nice example here.  Or am I telling myself a narrative fallacy?

For what it's worth, I don't think that a pandemic that has reached full flow is very compatible with the mathematical definition of a chaotic system - it has some but not all of the elements, and the attractor is not very strange.

There are a few papers on the pandemic and chaos theory, but it doesn't seem to be gaining much traction. 

Rom had this to say:

"However a lot of the variation outside of the longer trends might just as well be the result of a chaotic mishmash of thousands of variables, and quite a random process."

The fallacy here is the idea that we're at the mercy of thousands of random variables.  Sure - there is randomness everywhere, especially in the early stages of each wave that starts at a low baseline.  However, lots of definable and measurable events have been clearly shown to influence the rate of spread of the pandemic - levels of ventilation, duration of close contacts, levels of PPE use, frequency and size of mass events, variations in the outside temperature.  It's all there, evidenced and known. Measurable and quantifiable and controllable, should we wish to do so.

As it is, about half the variance outside the longer term trends seems to be down to the weather....  Which, to be fair, has a lot of overlap with chaos theory so perhaps I am foolish to write off chaotic effects in the later stages of a pandemic!  Edit:  Not so foolish really, as the pandemic is following the weather in a simple way, it would only itself be chaotic if it was influencing the weather as well as following it...

Post edited at 22:08
In reply to wintertree:

> What's notable about this is that a totally unrelated poster was insisting on much the same take during plotting #39 by drawing an analogy to financial markets (e.g. "Covid looks to me to have similar properties to turbulent markets")

My basic point still stands.

Covid is a virus which only crossed into humans in 2019.  It has already had two major mutations since the initial pandemic wave (alpha and delta) each of which was more infectious than the last.

Vaccinations are also a new and rapidly changing technology.  We've got at least three fundamentally different vaccination technologies and the mRNA vaccines are themselves quite new.  

There are a whole bunch of non-vaccine Covid-countering technologies - testing, masks, medicines, air conditioning, cleaning/surface treatment products - which are receiving massive funding and we can expect to rapidly improve and change.

And finally we have politicians and their sometimes crazy policy developments.

Like financial markets such as crypto or tech shares we should expect unpredictable events from virus mutation, technology shifts or political craziness, and these could easily be 'unknown unknowns' which suddenly drown out the known effects which we have studied in the year and a half of data we have so far.

My point was not about how well we have analysed and found relationships in the year and a half of data it is about whether a year and a half of data is enough to be able to confidently predict what will happen in the future.

> and arguing that this would likely dominate the data, particularly away from long term trends going forwards.

I'm going to say that it is more likely than not that some effect or event not captured in the data today will dominate the data in the future.  There are so many ways this could happen that if you add the probabilities it is going to be over 50%:

a. Virus gets a mutation which is super infectious but has fewer health consequences and the pandemic ends by everyone catching the new variant and becoming immune to the more serious variants.

b. Someone comes up with a medicine which is so effective nobody is worried any more because if you catch it you just take a few pills.

c. One of the vaccine guys tweaks their product or finds a new schedule/dose or mix of vaccines which is pretty much 100% effective.

d. We get financial instability caused by Brexit and the money printing for Covid spending and everything turns to sh*t because debt run up during Covid starts to force companies out of business, people out of their homes and cuts in public spending on health.

e. The death of a famous person from Covid or a vaccine side effect shifts public opinion on vaccination, masks or medicines in a dramatic way.   

6
In reply to wintertree:

> There were several people on here and plenty elsewhere making a lot of noise about very low probability side effects from the AZ vaccine, that were orders of magnitude lower than the risk posed by the virus at its then levels, let alone what's happened since.

The fact that a car is orders of magnitude better than walking isn't a reason for choosing  a Ford instead of a BMW.

> All those voices have been and remain silent over the parallel circumstance with Pfizer.  Whilst it appears to be a lower risk side effect, the benefit of the vaccine in the young is orders of magnitude lower, so the same questions arise.  

Obviously, if there is some Pfizer side effect which is much worse for young males that's a good reason for using a different vaccine on young males.  I'm not going to argue any different.    

I only started talking about AZ vs Pfizer because somebody posted the side effect data and I was taken aback by how much higher the numbers for AZ were.  I don't spend my life chasing down this stuff, I react to what I happen to see.

My guess, as I said in an earlier post, is that unless they have a significant breakthrough, AZ will scale down and exit this business or sell it off because it is tying up valuable resources, they aren't making any money and their main competitor is making a ton of money and using that funding to grow their R&D and manufacturing capability making it more expensive to keep up.   It's normal to have a shake-out in tech industries after it becomes clear which products are most successful in the market.

1
 Šljiva 26 Aug 2021
In reply to tom_in_edinburgh:

My guess, as I said in an earlier post, is that unless they have a significant breakthrough, AZ will scale down and exit this business or sell it off

Already said in July they were exploring options for vaccine business, clarity expected by end of year 

OP wintertree 26 Aug 2021
In reply to tom_in_edinburgh:

My comments on AZ were in relation to the “Rom” like pop up poster who spent several months pushing a very one sided view over the risks at a time when vaccination was directly saving lives and curtailing growth of the virus - saving many more lives.  They aren’t the only person to have had a one sided view of side effects, mind.

>  AZ will scale down and exit this business or sell it off because it is tying up valuable resources, they aren't making any money and their main competitor is making a ton of money and using that funding to grow their R&D and manufacturing capability making it more expensive to keep up.  

This rather overlooks the dramatic differences in the supply chains for the DNA vaccines and the synthetic vesicle mRNA vaccines.   Their costs and scalability are by no means equal. 

You may not have noticed, but AZ have started trials for their platform against an unrelated disease.  It also seems likely that the cause of their main side effect has been identified and is eminently fixable.  As a platform technology, the basis for their vaccine is incredible 

It was the choice of Oxford and AZ not to make any money - perhaps their management felt that making “a then of money” out of a global health crisis was the wrong thing to do.  If they do sell their vaccine technology on as a going concerns - already on the table - they will have changed the world for the better and will get their rewards not from the people blighted by covid but from investors.  It’s an admirable approach.  Likewise, in transferring their knowledge on producing this platform to the SII in India, they have got the world’s largest producer through almost all the hoops to cranking out other vaccines based on their platform technology.  The production capacity there is phenomenal.  This was done on a non profit basis and is directly helping a mind boggling number of people - largely in developing nations - with the output levels from SII.  Having a licence manufacturer already set up and proven capable of rapid regulatory approval adds way more value to a sell off of the vaccine business; again they’re looking forwards to future profit from investors whilst helping people at no profit.  It is a powerful remind that businesses do not have to be profit driven on all timescales.

> My point was not about how well we have analysed and found relationships in the year and a half of data it is about whether a year and a half of data is enough to be able to confidently predict what will happen in the future.

And my point was not rehash that argument.  I have nothing to add, and it’s always been obvious that everything is going to change in the future.  Things Will Happen.  Good working getting Brexit in to your updated position though.

My point was that it was one of those odd coincidence that two different posters come along making the same (IMO deeply flawed) analogy to a random and chaotic financial system.

Edit: One bite…

> I'm going to say that it is more likely than not that some effect or event not captured in the data today will dominate the data in the future

Yes I readily and repeatedly agreed with this; just as such events have “dominated” the past.  The weather effects *modulate* in the medium frequency whatever long term, low frequency signal is “dominated” by the other effects.  Given the different frequency bands, as longs as there’s transmission going on, unless the effect breaks the weather link, I expect it to continue to *modulate* the baseline.  None of the reasons you gave would I expect to break it other than elimination.  Indeed, many of the reasons have already been seen, and can be seen to change (“dominate”) the baseline, with weather modulation still being visible in the medium frequency band even as those effects drive change in the baseline.  

Post edited at 08:40
1
 David Alcock 26 Aug 2021
In reply to Šljiva:

"but that's sadly not legal here."

Never stopped most fruit growers I know round here... 

 David Alcock 26 Aug 2021
In reply to MG:

I used to lash three 18 & 1/2' Bratt's ladders* in a tripod and just 'walk' it around.

(Dibnah-style steeplejack ladders) 

In reply to wintertree:

>   None of the reasons you gave would I expect to break it other than elimination.  

Elimination or elimination in rich countries are what I would consider the most likely outcomes.

When we get to the point of giving hundreds of millions of people jags which stop most serious disease inside a year and a half I'm going to bet the people who did that will come out with something even better next year.

OP wintertree 27 Aug 2021
In reply to Longsufferingropeholder:

> Looking warm this week. I'm going to predict {gasp} a drop in rates coming soon.

Latest update to the English rate constant plot has bobbed down to notable decay for the first time in 3 weeks.  That last data point can always be provisional if there's a bit more lag than normal in the reporting systems....

Growth in Scottish cases is starting to plateau perhaps, certainly the rate constant as measured a week-on-week comparison(*) is continuing its drop towards y=0 and then decay.  One of the possibilities chewed over was the "switch on" of asymptomatic testing feeding through to PCRs as schools returned; this never really fit with the timing of the rise (a bit too soon for that perhaps) nor the demographic (most aggressive rise in ages 20-24).  The hospitalisation data is now rising right when we'd expect it to track a rise in real infections  My suspicion still lies on unsustained rush to nighclubs after they reopened perhaps not unlike England going off various news reports of opening nights vs now.  All a guessing game unless some epidemiologists working the full data put out a media quote or similar.

(*) Such a measurement doesn't turn to decay until the data has been in decay for a full week - fitting to the cases-curve or eyeballing the trendline can show decay before then, but these methods produce a much worse measure of the rate constant due to day-of-week effects that drop out of the week-on-week measure.  No unsquarable circle here, the 7-day measure is best considered as applying to a period of a week centred on the middle of that measurement interval, so it effectively lives 3.5 days behind the leading edge of the cases curve.  That leading edge looks mighty like it might have plateaued to my eye; of course school based transmission is now kicking in to the data and could pivot the curve back up.


In reply to wintertree:

> Latest update to the English rate constant plot has bobbed down to notable decay for the first time in 3 weeks.  That last data point can always be provisional if there's a bit more lag than normal in the reporting systems....

> Growth in Scottish cases is starting to plateau perhaps, certainly the rate constant as measured a week-on-week comparison(*) is continuing its drop towards y=0 and then decay.  One of the possibilities chewed over was the "switch on" of asymptomatic testing feeding through to PCRs as schools returned; this never really fit with the timing of the rise (a bit too soon for that perhaps) nor the demographic (most aggressive rise in ages 20-24).  

Scottish Government are talking about schools.

"Asked about schools, he said: “Cases have risen very significantly within Scotland and we are looking closely at why that is the case.

“Undoubtedly the gathering of people together in schools will have fuelled that to some extent. You can see that in the proportion of younger people who are testing positive.”"

https://www.thenational.scot/news/19535807.covid-scotland-school-closures-a...

OP wintertree 27 Aug 2021
In reply to tom_in_edinburgh:

I’m sure schools contributed but given where the biggest rise is (20-24) and the inclusion of non school age adults (18-19) in the next highest growth bin (by rate constant growth), it’s astoundingly clear that the centre of growth is *not* in schools.  Likewise rising cases landed to soon to be schools.

It’s very convenient for the Scottish government to be able to point at schools with a very weak statement (“… to some extent”) because people will swallow it and not question further, when the data is clear that something else must be going on, and the timing is pitch perfect for that something to be the most recent dropping of restrictions - restrictions with a strong demographic tie to the rise.

Post edited at 17:28
1
In reply to wintertree:

> It’s very convenient for the Scottish government to be agile to point at schools with a very weak statement (“… to some extent”) because people will swallow it and not question further, when the data is clear that something else must be going on, and the timing is pitch perfect for that something to be the most recent dropping of restrictions - restrictions with a strong demographic tie to the rise.

It's not convenient at all.  Their whole policy has been to keep schools open and to downplay spread in schools.  It is far harder for them to blame the rise on schools than on nightclubs.   If they thought this was mostly nightclubs they'd shut nightclubs and the political cost of doing so would be low.  If they need to shut schools the fallout will be far larger.   People don't have to stay off work because their kids can't go to nightclubs.

3
 elsewhere 27 Aug 2021
In reply to wintertree:

Thanks for the update today.

OP wintertree 27 Aug 2021
In reply to tom_in_edinburgh:

But there’s likely no need to close anything if the growth peaks and if hospitalisations reflect the major demographic shift they brought, so if they can blame the current rise on something everyone is behind reopening instead of something a lot of people were against reopening it’s a win/win - no action is needed and attention is diverted from the less popular and riskier policy decision…

I don’t normally get drawn in to speculating on the motivation of political takes as I’m utterly clueless in politics and it’s all bollocks anyhow, but that statement was a very weak blaming of schools really.

Edit: Also if it was schools, why would the rate constant start collapsing back down almost immediately, especially given that there’s little vaccination in school aged children?  Does not compute.

Post edited at 17:59
 Wicamoi 27 Aug 2021
In reply to wintertree:

> I’m sure schools contributed but given where the biggest rise is (20-24) and the inclusion of non school age adults (18-19) in the next highest growth bin (by rate constant growth), it’s astoundingly clear that the centre of growth is *not* in schools. 

I completely agree.

> It’s very convenient for the Scottish government to be able to point at schools with a very weak statement (“… to some extent”) 

But here I disagree with your interpretation (athough I emphasize that i am not at all supporting the point that somebody-in-someplace was trying, and failing, to make). It was not "the Scottish government" in general, but the education secretary (John Swinney) in particular who made the reported comments. And he made them in direct response to a question about the role of the reopening of schools in the recent rises in Covid cases. Seen in that context I think his response is pretty fair and straightforward. His foremost agenda would likely be to keep schools open, rather than to blame the rise in cases on them in order to divert attention from other policies that may have influenced the rise in cases.

Disclosure A: I despise nationalism, but i have voted SNP tactically in the past and might well vote for Independence in the future.

Disclosure B: I have met John Swinney, and found him both very likeable and rather impressive.

Finally, thanks for your updated plots. You know that I particularly appreciate your efforts on Scotland. I must say though, I wish there were advocates for Northern Ireland too.

1
OP wintertree 27 Aug 2021
In reply to Wicamoi:

Point taken - thanks.  As I said I'm pretty clueless on the political interpretation (doubly so beyond England) so I appreciate you taking the time to give the context and your interpretation.  I'm too used to asking what the real reason for the Westminster lot doing or saying anything actually is...  Don't have to project that everywhere...

A quote from a recent BBC article on the area:

Sage (Scientific Advisory Group for Emergencies) says it is still difficult to work out whether schools are drivers of transmission, or simply reflecting the spread of the virus in the communities where they are located.

https://www.bbc.co.uk/news/health-58357021

Lots of uncertainty ahead around schools reopening.  It's a shame both England and Scotland bin the cases data in chunks that do not align to school ages, with the 15-19 chunk being particularly muddled.  I suppose (hope???) higher powers have access to better data than that...

>  I must say though, I wish there were advocates for Northern Ireland too.

If there'd been much interest I'd run off a more full suite of plots.  I think interest in the threads is fading now, if we start to see the infection and hospitalisation of unvaccinated tailing off over the next few weeks and a less-than-corresponding rise in admissions of vaccinated, I think it's going to plummet further; hopefully draw a line under a weekly thread by #52 as we all move on.  To winter...

 Wicamoi 27 Aug 2021
In reply to wintertree:

> Point taken - thanks.  As I said I'm pretty clueless on the political interpretation (doubly so beyond England) so I appreciate you taking the time to give the context and your interpretation.  I'm too used to asking what the real reason for the Westminster lot doing or saying anything actually is...  Don't have to project that everywhere...

Yes, this endlessly depressing, dishonest, partisan, and corrupt government in Westminster can wear all of us out - or those of us that don't support it at least - and make us cynical, and it is partly for that reason that i wanted to say something less cynical about the government in Scotland. No government is remotely perfect of course!

> >  I must say though, I wish there were advocates for Northern Ireland too.

> If there'd been much interest I'd run off a more full suite of plots.

It would have been nice to see a bit more informed discussion on the NI version of the pandemic. Could have been instructive - still could be - on the scope of governmental/political influence on the impact of Covid.

 I think interest in the threads is fading now, if we start to see the infection and hospitalisation of unvaccinated tailing off over the next few weeks and a less-than-corresponding rise in admissions of vaccinated, I think it's going to plummet further; hopefully draw a line under a weekly thread by #52 as we all move on.  To winter..

Well, here's to hoping it's all become boring enough by #52 that #53 is unnecessary. I'll likely still miss them though.

Post edited at 23:57
In reply to wintertree:

> Edit: Also if it was schools, why would the rate constant start collapsing back down almost immediately, especially given that there’s little vaccination in school aged children?  Does not compute.

I think there's more to the start of term than just the day kids return to school and some activities are likely to be more compressed into the last few weeks of holiday than in a normal year because of the removal of restrictions which were in force at the start of summer holidays.

Families are going to arrange holidays with a view to being back before the start of term.  The travel involved is a risk and the testing needed to travel is likely to find asymptomatic cases.

Kids are going to notice the holidays are about to end and try and get some fun activities done before it happens.  Contacts with school friends in older kids are probably going to increase the last week or so before the term starts.  There's going to be back to school shopping.

Kids have parents and siblings and kids in S5/S6 have friends at Uni. Siblings a few years older than a kid in S5/S6 could easily be in their twenties as could parents of kids in primary.   Handing out lateral flow tests to everybody at school is going to result in positives which cause people in their twenties who are friends/siblings/parents of school age kids to take tests.

3
 DundeeDave 28 Aug 2021
In reply to Wicamoi:

John Swinney isn't education secretary anymore. 

 Si dH 28 Aug 2021
In reply to tom_in_edinburgh:

That's some fantastic straw-clutching.

As I read the PHS dashboard (which I confess to finding a bit difficult because of the way the data is presented) the age demographic actually seems to have shifted again in this last week. The original cause of the current wave was definitely something in young adults but this week the number of cases from 15+ seems to have flattened off and in the 0-14 group to have risen significantly. This fits well with the interpretation  in the quote about sage above that suggests case rates in schools might be "simply reflecting the spread of the virus in the communities where they are located."

To Wicamoi: as per another post above, Swinney is now "Cabinet Secretary for Covid Recovery" whose job is presumably therefore to plan and then defend the covid roadmap in Scotland. He has an obvious incentive to point blame towards something (schools) that might have caused cases to rise but about which very few people would disagree with the Government's approach anyway. Whether that's what he was actually doing, I don't know. But given his role, if he was being honest, then he has a poor grasp of the data.

 Si dH 28 Aug 2021
In reply to wintertree:

Unfortunately I think it's likely the apparent England-level week-on-week decline near the leading edge that you reported yesterday has been brought about because cases in the south west have dropped lots in the last few days after their recent spike, rather than by any broader turning point. In fact cases in the North East now seemed to have turned upwards again and cases elsewhere (outside the South West, and London where rates are falling) are generally following previous trends.

Post edited at 08:41
 BusyLizzie 28 Aug 2021
In reply to wintertree:

>   I think interest in the threads is fading now, if we start to see the infection and hospitalisation of unvaccinated tailing off over the next few weeks and a less-than-corresponding rise in admissions of vaccinated, I think it's going to plummet further; hopefully draw a line under a weekly thread by #52 as we all move on.

I still find these threads are a lifeline. I get that at some point it will be right to change the frequency, not least because you must need a rest! Thank you for coninuing for so long.

OP wintertree 28 Aug 2021
In reply to Si dH:

Thanks; the decay spike in the rate constants plot is more negative than the rise; that’s unusual for a punctuate event like the SW event (festival?) - normally for those the extra-high point on the rate constant plot has a clear matched extra-low a week later.  So perhaps that’s part of the change (as much as half, perhaps) but there’s other stuff going on taking the national level data in to decay as well.  

I agree re: straws and schools - just had a look at travellingabby’s plot of the data and it does look like the rapid exponential growth in 20-24 is tapering a lot more than the slower exponential growth on the oldest <20 age band.  The timing of the young adult spike couldn’t have been worse to prime cases going in to schools.  

On the general subject, it’s interesting that there’s been a lot of press noise anticipating a JCVI decision on offering a single dose of Pfizer to those aged 12-15.  We’ll see where that goes, and if the costs to the child of educational disruption factor in to their decision - it seems very wrong how the school children end up carrying the consequences of adults using their freedom to be responsible time after time.  I suppose we don’t know how much disruption there’s going to be this term with changes to isolation rules.

1
 Offwidth 28 Aug 2021
In reply to wintertree:

A recent report cataloguing how governments across the world used the pandemic to constrain public freedoms well beyond public health requirements. 

https://www.article19.org/gxr-2021/

1
 Offwidth 28 Aug 2021
In reply to wintertree:

Plus Bloomberg comments on an Israel based preprint (not peer reviewed) claiming that results show being infected previously (in Jan /Feb) gives better protection against Delta infection than Pfizer double vaccination. It would be good if anyone who knows of any independent analysis of these results (on Twitter etc) could link it.

https://www.bloomberg.com/news/articles/2021-08-27/previous-covid-prevents-...

https://www.medrxiv.org/content/10.1101/2021.08.24.21262415v1.full.pdf

Post edited at 09:32
 Offwidth 28 Aug 2021

In reply:

Plus a criticism of CDC data collection on breakthrough cases:

https://www.theguardian.com/commentisfree/2021/aug/06/cdc-covid-coronavirus...

 Wicamoi 28 Aug 2021
In reply to Si dH and Dundee Dave

I accept the correction regarding Swinney's move from Education in the the spring, and apologise for my failing memory! But again, given that he was directly asked about the role of schools, his response

"Cases have risen very significantly within Scotland and we are looking closely at why that is the case. Undoubtedly the gathering of young people together in schools will have fuelled that to some extent. You can see that in the number of young people who are testing positive"

Is that incorrect or misleading? The "to some extent" is a vague, but not unreasonable modifier. I don't think anyone listening to that would take away the message that schools are effectively responsible for the rise in cases, but people seeing it reported in a particular way obviously can. A lot of meaning could be conveyed by the way he said "to some extent" - anyone heard the interview?

Ideally he should have gone on to say that cases are rising fastest in young adults, and it is clear that the spike did not originate in schools. For all we know he did but it was not reported, or was about to do so but was interrupted by another school-related question from the interviewer. It might not be so easy to come up with a perfectly true and accurate phrase that cannot be misinterpreted with a small shift in context or editing.

But perhaps I am being biassed by my personal liking for the man. Anyway, it's all a rather minor point about cynicism really, and I'm not here to defend the SNP!

 Šljiva 28 Aug 2021
In reply to wintertree

if it’s not the schools wot done it in Scotland,  presumably we won’t see a similar spike here in the next couple of weeks. As we’re certainly being primed for a big back-to-school spike ( see headlines last couple of days) then no doubt the govt will claim all the success. Or maybe I’m just getting too cynical?

OP wintertree 28 Aug 2021
In reply to Šljiva:

> if it’s not the schools wot done it in Scotland,  presumably we won’t see a similar spike here in the next couple of weeks.

I imagine cases will spike with back to school here, but I'll eat my hat if we see an unprecedented 3-day doubling time in ages 20-24 as a result of schools returning.  I hope we'll see a more moderate rise more concentrated in younger ages.

The return to universities however, that's a wild card.  There seems to be a lot of gung ho thinking about in-person teaching in a "back to normal" sense, along with no interest in vaccine mandates etc.

> As we’re certainly being primed for a big back-to-school spike ( see headlines last couple of days) then no doubt the govt will claim all the success. Or maybe I’m just getting too cynical?

It's really hard to get the calibration of my cynicism dialled in to the right zone.  Too much is as bad as too little.

1
In reply to Si dH:

> That's some fantastic straw-clutching.

The straw clutching is trying to explain a massive spike in cases based on events like nightclub reopening which involve relatively small numbers of people when an event like schools restarting which affects very large numbers of people is staring you in the face.

5
 Misha 29 Aug 2021
In reply to wintertree:

I think in England it’s Paugust - you said weeks ago that rates were going to pogo around and that’s what’s been happening. It’s good to see that case numbers have levelled off and are falling a bit but in the scheme of things they are just moving around with a range of 25-40k a day (official cases, that is). Which is still a lot but if that continues to translate to a tad under 1,000 admissions a day, I guess it’s manageable.

The big question is when will it burn out to low thousands of cases a day, if ever. Depends on level of vaccine escape / reinfection. 

Seems reasonable to expect cases to go up in September due to schools and then unis. Wouldn’t be surprised to see 50-60k a day.

Your explanation for Scotland makes sense. Also the absolute numbers are much lower, so the impact of a few superspreader events will be greater. Similar thing in the SW after that festival.

1
 Misha 29 Aug 2021
In reply to tom_in_edinburgh:

However the school leaving age is 18… and that’s not where the initial spike was. The thing with nightclubs is not everyone needs to go. One person can pick it up there, then a few days later pass it on to a few of their mates by sitting round a small table in a pub or indeed in someone’s living room. Younger people tend to socialise more so it can spread like wildfire. 


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